I can't answer your question other than to say I've
found other incompatabilities with OS 3.9.
I would guess if you boot in OS 3.1 and set the 2.5
drive to be non-bootable then OS 3.9 might see it.
I finally went back to OS 3.1 on my A2000 because of
the warm-boot problem.
On my A3000 I have an external SCSI drive box and under
OS 3.1 I could turn it on or off whenever I needed it.
Under OS 3.9 I can't do that anymore. If its not turned
on at cold-boot then it WILL not mount.